Filtered or unfiltered coffee increases homocysteine levels in healthy individuals whereas caffeine has a much weaker effect on homocysteine levels. Stopping drinking coffee reduces homocysteine levels.
Increased homocysteine levels point to decreased levels of L-cysteine which is synthesized from homocysteine. With decreased synthesis of L-cysteine iron-sulfur cluster formation could be dysregulated which could upset many biological processes. Increased homocysteine levels could could affect DNA methylation. In schizophrenia there is a positive association between plasma homocysteine and DNA methylation. Difficulties due to coffee could take years to develop due to hypermethylation of genes taking years to develop.